When I would ride the subway in DC, in uniform, I was a magnet for random schmoes who, based upon their 3 years of service as an enlisted man 2 or 3 decades earlier, fancied themselves sufficiently versed in national security strategy to give me their opinions and a) thought that I would actually care and b) seemed to think that I was in a position to make changes that they recommended. If I were to critique the specific borders chosen by DoD or State, I would feel like I am turning into "that guy." But on the general issue of whether two organizations should stovepipe their organizations or create overlap, I think overlap makes more sense. If you get DoD and State with the same AORs, then you increase the tendency for them to view things in terms of their AORs with less regard to the big picture. More troubling, you increase the tendency for them to think alike. When they overlap, you can create a climate in which State is telling DoD, "your Afghan-Pakistani border games are complicating our India-Pakistan initiatives" while DoD tells State, "your India-Pakistan initiative is very quaint, but we've got a war to deal with here on the Afghan-Pakistani border and it is intricately linked to our conflicts elsewhere in CENTCOM."

At risk of becoming that guy on the subway, I think it makes a whole lot of sense for State and DoD to have different AORs in the India-Pakistan region, first off, for the reasons stated above (stovepiping versus overlap to spur different thinking and bigger picture perspectives). Second, barring some event of world historical significance, we're not going to be conducting major combat operations in India. We are already conducting routine air strikes in Pakistan, I would not be surprised if we routinely conduct special operations in Pakistan, and this is directly related to activities occuring elsewhere in CENTCOM. On the other hand, the diplomacy issues on the subcontinent have much more to do with Afghanistan, India, and Pakistan and much less to do with Iran or the Arab world.

Full disclosure: my degree is in biology and I never served at an echelon above battalion (but now I'm gloating!).